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Solutions for data integration in functional genomics: a critical assessment and case study

D. Smedley, M. A. Swertz, K. Wolstencroft, G. Proctor, M. Zouberakis, J. Bard, J. M. Hancock, P. Schofield
2008 Briefings in Bioinformatics  
We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen.  ...  the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics.  ...  As things stand, the proposed solution for our case study remains the only practical one for highthroughput, generic, distributed analysis.  ... 
doi:10.1093/bib/bbn040 pmid:19112082 fatcat:6hoxfuktznhkbcfemik2rb4jqq

Translational genomics

Martin Kussmann, Jim Kaput
2014 Applied and Translational Genomics  
the best science into applications and solutions for human society.  ...  Recent scientific and societal developments have triggered a re-assessment of the connotation that "translational" and "basic" are either/or activities: translational research nowadays aims at feeding  ...  Classical case/control designs of human clinical/nutritional intervention studies should be complemented by crossover, longitudinal studies, in which every subject is its own case and control (Kaput and  ... 
doi:10.1016/j.atg.2014.05.001 pmid:27284502 pmcid:PMC4886729 fatcat:tagonpycd5afthuygvzcrwld6u

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio

Teri A. Manolio
2016 Atherosclerosis  
, and diffficulties in integrating genomic results into electronic medical records.  ...  In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine.  ...  Initiated in 2013, IGNITE is developing, assessing, and disseminating successful genomic medicine practice models that integrate genomic data seamlessly into the EMR and deploy clinical decision support  ... 
doi:10.1016/j.atherosclerosis.2016.08.034 pmid:27612677 pmcid:PMC5064852 fatcat:ilm6n5x4onbxrkjqqgroidtwa4

The 4th Bologna Winter School: Hot Topics in Structural Genomics

Rita Casadio
2003 Comparative and Functional Genomics  
The school provided an opportunity for students and scientists to debate current problems in computational biology and possible solutions.  ...  The course, co-supported (as last year) by the European Science Foundation program on Functional Genomics, focused mainly on hot topics in structural genomics, including recent CASP and CAPRI results,  ...  Therefore, integrated knowledge will help us in solving the folding problem also on a genome-wide scale.  ... 
doi:10.1002/cfg.314 pmid:18629078 pmcid:PMC2447363 fatcat:2pe2f74zcjainlb3e6rwycwpce

Integrating Genomes

D. R. Zerbino, B. Paten, D. Haussler
2012 Science  
Using genomics data to model genome evolution, mechanism, and function is now the heart of a lively field.  ...  of these data will be of critical importance.  ... 
doi:10.1126/science.1216830 pmid:22499938 fatcat:pkraq26dpzehreooeka2k7tlyi

Computational structural genomics

Igor V. Grigoriev
2001 Proceedings of the 2001 ACM symposium on Applied computing - SAC '01  
Since solving a structure is time-consuming and expensive, choosing the right targets for structural studies becomes important.  ...  existing in nature in order to infer protein molecular functions.  ...  In this case, disulfidebonds formed by cysteine residues (Cys) provide the alternative for structure solution.  ... 
doi:10.1145/372202.372269 dblp:conf/sac/Grigoriev01 fatcat:kfxptvf3cjbtzpxl2m4mzdt7vq

Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration

Timothy Reynolds, Emma Johnson, Spencer Huggett, Jason A. Bubier, Rohan H. C. Palmer, Arpana Agrawal, Erich J. Baker, Elissa J. Chesler
2020 Neuropsychopharmacology  
Fig. 1MULTISPECIES GENOMIC AND EPIGENOMIC DATA INTEGRATION.: Genetic variation, gene regulation, and homology datasets are retrieved from a variety of publicly available resources and data repositories  ...  Scalable computing, new data integration strategies, and advanced analysis methods outlined in this review provide a framework to efficiently harness model organism data in support of clinically relevant  ...  ACKNOWLEDGEMENTS The authors thank Stephen Krasinski of The Jackson Laboratory for assistance with this manuscript.  ... 
doi:10.1038/s41386-020-00795-5 pmid:32791514 fatcat:hpg4ondgvjdmdgdxm3x4hgmw2m

Genomic Privacy (Dagstuhl Seminar 15431)

Jean Pierre Hubaux, Stefan Katzenbeisser, Bradley Malin, Gene Tsudik, Marc Herbstritt
2016 Dagstuhl Reports  
Impressive recent advances in genome sequencing have ushered a variety of revolutionary applications in modern healthcare and epidemiology.  ...  A digitized genome represents one of the most sensitive types of human (personal) identification data. Even worse, a genome contains information about its owner's close relatives.  ...  We have been researching on avenues which preserve the desired functional evolution, but satisfy the need for built-in, by-design privacy, integrity and availability of such critical data.  ... 
doi:10.4230/dagrep.5.10.50 dblp:journals/dagstuhl-reports/HubauxKMT15 fatcat:exg6k3rcezf6jifhxpj5ml4gye

Pharmacovigilance in a genomic era

P Farahani, M Levine
2006 The Pharmacogenomics Journal  
for data collection, production, and storage that is necessary to use this information in developing effective health care solutions.  ...  Beyond the importance of harmonization of data both within the genomic banks (the NBAC report) and within the administrative health record databases (such as GPRD), it is also critical that data for the  ... 
doi:10.1038/sj.tpj.6500370 pmid:16415916 fatcat:32dyp3agvzcjbnpwhskxds4xye

Marine ecological genomics: when genomics meets marine ecology

S Dupont, K Wilson, M Obst, H Sköld, H Nakano, MC Thorndyke
2007 Marine Ecology Progress Series  
'what is the relationship between community structure and ecological function in ecosystems?'; 'how can a species and the phylogenetic relationship between taxa be identified?'  ...  In this review we explore the potential and promise offered by genomics, genome technologies, expressed sequence tag (EST) collections, microarrays, proteomics and bar coding for modern marine ecology.  ...  The inclusion of 'function' is critical because the goal is to understand what genes/ genomes and their variants do at higher levels of integration.  ... 
doi:10.3354/meps332257 fatcat:l5l47zp2njf4zlbixvsl6b5dmu

Computational genomics

Eugene V Koonin
2001 Current Biology  
as the structural basis for a critical biochemical activity.  ...  Such a young field is already quite diverse, and in this short article I will concentrate on several issues that seem to be critical for deciphering biology from genome sequences, rather than mathematical  ... 
doi:10.1016/s0960-9822(01)00081-1 pmid:11267880 fatcat:27qnnc4jlfdgphdwnispxu2ree

Whole-genome haplotyping approaches and genomic medicine

Gustavo Glusman, Hannah C Cox, Jared C Roach
2014 Genome Medicine  
The main approaches for phasing genomic sequence data are molecular haplotyping, genetic haplotyping, and population-based inference.  ...  Here, we review advances in whole-genome haplotyping approaches and discuss the importance of haplotypes for genomic medicine.  ...  GG and JCR received support from and the National Institute of General Medical Sciences Center for Systems Biology (P50 GM076547). We thank the anonymous reviewers for their contributions.  ... 
doi:10.1186/s13073-014-0073-7 pmid:25473435 pmcid:PMC4254418 fatcat:3cwkvkr4k5bfba3cobsey4mphq

Integrated Metabolomics and Genomics

Svati H. Shah, Christopher B. Newgard
2015 Circulation: Cardiovascular Genetics  
Integration of metabolomics, genetics, and other omics platforms in a systems biology approach holds potential for elucidating novel genetic markers and mechanisms for cardiovascular disease.  ...  We review important studies that have used metabolomic profiling in cardiometabolic diseases, approaches for integrating metabolomics with genetics and other molecular profiling platforms, and key studies  ...  Sources of Funding Work cited in this article was supported by National Institutes of Health grants HL095987 (Shah) and P01-DK58398 (Newgard) and by a sponsored research agreement from Pfizer.  ... 
doi:10.1161/circgenetics.114.000223 pmid:25901039 pmcid:PMC4408557 fatcat:ubp6sysxhnekjlffcexdwydzku

Genomics and plant cells: application of genomics strategies to Arabidopsis cell biology

M. Bevan
2002 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Among these are organizational changes needed to create common datasets accessible to all scientists, and bioinformatics solutions to capture and integrate diverse datasets.  ...  In this review I seek to describe how the complete catalogue of plant genes and proteins, revealed by genome sequencing, can provide novel insights into cell biology.  ...  A relatively straightforward example of data integration illustrates the type of work remaining to be implemented on a genome-wide scale in Arabidopsis.  ... 
doi:10.1098/rstb.2002.1084 pmid:12079668 pmcid:PMC1692991 fatcat:amyqbgap3jasjmvmhxlfxmxxei

Genomics in cardiac metabolism

J.L. Samuel, M.C. Schaub, M. Zaugg, M. Mamas, W.B. Dunn, B. Swynghedauw
2008 Journal of Molecular and Cellular Cardiology  
Large-scale analysis of genome structure, gene expression, and metabolites are new technologies available for studying cardiac metabolism in diseases known to modify cardiac function.  ...  These technologies have several limitations and this review aims both to assess and take a critical look at some important results obtained in genomics restricted to molecular genetics, transcriptomics  ...  Swiss Heart Foundation, Novartis Foundation, Fifth Frontiers in Anesthesia Research Award from the International Anesthesia Research Society, BBSRC, and EPSRC in the UK.  ... 
doi:10.1016/j.yjmcc.2008.02.230 fatcat:ej5hklg5izhzjoadhgvzr4papm
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